The Genotype-Tissue Expression (GTEx) project

By J. Lonsdale, Jeffrey A. Thomas, Mike Salvatore, R. Phillips, E. Lo, Saboor Shad, R. Hasz, Gary Walters, Fernando García, N. Young and 117 more. Nature Genetics, 2013

8,629 citations recorded by the source corpus.

Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d868486f256994e1a6a7c94780af714f2974ecc7

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Citations in the corpus

FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations (2022, background): “Because preprocessed TPM values are not available after last update of the GDC portal, raw RNAseq read counts were downloaded and edgeR was then used to calculate TMM values from read counts (34).”
The Application of Deep Learning in Cancer Prognosis Prediction (2020, methodology): “The Genotype-Tissue Expression (GTEx) database contains whole-genome sequencing and RNA-sequencing profiles from ~960 postmortem adult donors of many tissue samples that have tissue images stored in an image library for public access [25,26].”
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, methodology): “Gene–enhancer associations were generated based on five methods: eQTLs (45), eRNA co-expression (22), TF co-expression, capture Hi-C (CHi-C) (30) and gene target distance, all of which are described in the Supplementary Methods.”
Expression Atlas: gene and protein expression across multiple studies and organisms (2017, background): “uk/gxa/experiments?experimentSet=HipSci), Genotype-Tissue Expression (GTEx) version 6 (9), NIH Epigenomic Roadmap (10) (http://www.”
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans (2021, methodology): “We then used the GTEx database (21) to seek independent corroborating evidence of these putative junctions and found that reads corresponding to nearly one-third of these previously unknown junctions can be found within the GTEx data (table S7); this corresponds to >300,000 previously undefined vali”
The Landscape of long non-coding RNA classification (2015, neutral): “Lonsdale J, et al. The Genotype-Tissue Expression (GTEx) project.”